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Align pairs by edit distance (deprecated alias)

Source: R/align.R
align.Rd

align() is deprecated in favour of align_edit(): the generic name collides with Biostrings/IRanges exports in sessions that load both. It still works and returns identical results; new code should call align_edit().

Usage

align(pattern, text, smax = 64, with_cigar = TRUE)

Arguments

pattern

Character vector; query sequences (recycled to match text).

text

Character vector; reference sequences (recycled to match pattern). NA entries produce NA rows.

smax

Numeric; maximum edit distance searched, in [0, 511]. Pairs whose true distance exceeds it are unresolved by design.

with_cigar

Logical; if FALSE only scores are computed (cheaper, no traceback) and cigar is NA.

Value

See align_edit.